Comments (3)
Hey George, the compilation expects the compiled source directory for samtools and htslib, not the installation directory (even though that would be the correct way of doing things). I guess /apps/samtools/1.2.1 doesn't bam.h etc, but just the installed binaries, right? If you still have the samtools source directory, point LoFreq there. Or just install the binary distribution :)
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Thank you @andreas-wilm. I thought I would like to benefit from the new updates since the last binary release which was released a while back. Maybe you can compile a binary release for 2.1.3b? you could tag it as beta release. I would also be happy to test it and provide feedback.
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Coming soon...In the meantime see #28
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Related Issues (20)
- Issue during the make stage HOT 1
- lofreq_star-2.1.5_linux-x86-64 : ./lofreq: error while loading shared libraries: libhts.so.3 HOT 3
- Missing Variant with 90% AF HOT 2
- I have trouble to run bootstrap HOT 3
- ERROR in temp file HOT 1
- Meaning of normal_relaxed, tumor_relaxed, .._stringent (question)
- Using LoFreq-NQ? HOT 3
- Adding genotype information HOT 7
- Force overwrite
- Quality scores HOT 1
- Problem with "lofreq call"
- /bin/sh: line 1: 16782 Killed and CRITICAL [2021-11-30 08:43:03,767]: Following command failed with status 137 HOT 5
- No sample column
- Variants missing in parallel mode HOT 2
- lofreq p-value
- Warning: Didn't find any variants in input HOT 2
- Lofreq call-parallel applies filters with --no-default-filter option specified HOT 2
- lofreq call-parallel will hang forever on subprocess error
- Filter depend on number of cores?
- cpus count versus available cpus
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